Abstract
We use the bond fluctuation model BFM to study the pore-blockade times of a translocating
polymer of length N in two dimensions, in the absence of external forces on the polymer i.e.,
unbiased translocation and hydrodynamic interactions i.e., the polymer is a Rouse polymer ,
through a narrow pore. Earlier studies using the BFM concluded that the pore-blockade time scales
with polymer length as d N , with =1+2 , whereas some recent studies using different polymer
models produce results consistent with =2+ , originally predicted by us. Here is the Flory
exponent of the polymer; =0.75 in 2D. In this paper we show that for the BFM if the simulations
are extended to longer polymers, the purported scaling d N1+2 ceases to hold.We characterize the
finite-size effects, and study the mobility of individual monomers in the BFM. In particular, we find
that in the BFM, in the vicinity of the pore the individual monomeric mobilities are heavily
suppressed in the direction perpendicular to the membrane. After a modification of the BFM which
counters this suppression but possibly introduces other artifacts in the dynamics , the apparent
exponent increases significantly. Our conclusion is that BFM simulations do not rule out our
theoretical prediction for unbiased translocation, namely, =2+ .
Original language | English |
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Pages (from-to) | 014902/1-014902/10 |
Number of pages | 10 |
Journal | Journal of Chemical Physics |
Volume | 132 |
Issue number | 1 |
DOIs | |
Publication status | Published - 2010 |